So, it's your first year of grad school — congrats! But your first year is during a pandemic — yikes! Graduate school is stressful enough without having to worry about a deadly virus. Hopefully, this post will help you navigate through your first year by providing concrete advice for choosing your new lab and acclimating to a new workspace.
As a first-year STEM student, your school likely requires you to conduct research in various labs (usually 2-4) for a temporary period of time. After these rotations are complete, you will choose a lab as your new home for the next 4-7 years! It's an important choice to make, and you aren't alone if this process brings about some anxiety. Here are 10 tips to help ensure you arrive at the right decision.
1. Keep an open mind. You might arrive at your school with a PI or research topic in mind. Unfortunately, there are many factors at play that dictate what you will research other than your preferences. Have a Plan B and C just in case Plan A is not in your cards.
2. Shrink that chip on your shoulder. Its tempting to show-off and be over-competitive with your new lab mates. Don't. It's an awful way of making new friends. To be blunt here, your new co-workers don't care how smart you are. They want a lab-mate who is a hard-worker and helpful to work alongside. Be yourself. Save the energy you would spend on trying to impress others to do well at the tasks at hand.
3. Remember why you are there. The purpose of a rotation is to test out a lab. You are not there to churn out data, work long weeks, and publish a paper in a short amount of time. If you feel anxious or overworked during a rotation, imagine what five years in that lab will be like.
4. Ditch the "that's not how my old lab did it." saying. Your new lab will do things in new ways, and there might be a reason for that. When starting work in a new place, it's easy to get caught up in comparisons to the past. But this is a fresh start, embrace the changes and be willing to learn from your new lab-mates and mentors.
5. Ask about funding. $$$$. This point cannot be stressed enough. Just because a PI is taking on rotation students does not mean they have funding to bring you on as a full-time student. Before rotating with a PI, ask if they have money to cover your stipend. If they do not, consider rotating elsewhere. If a PI does not directly answer this question, they might be baiting you to get free labor.
6. Discuss potential thesis topics. Many labs treat students as employees. The students produce data like lab techs, and the thesis is an afterthought. Labs with this mindset are reluctant to let students graduate because they are precious cheap labor. It's important to have research expectations outlined before joining the lab as a student.
7. Speak to other students and faculty in the department. Check-in with others to learn about the reputation of the lab.
8. Ask about time off. Trust me; you need time off. The ideal answer to this question is, "of course, you can take vacations, just communicate with me first." Inquiring about vacation time is an imperative question if your family does not live nearby. Ideally, you should be able to take time off around the holidays and also have personal vacations.
9. Ask about the work schedule. Some labs have strict schedules; others are come and go. Your PI should not demand or coerce you to work more than 40 hours/week. Overtime is your choice.
10. Discuss career development with your PI. It's helpful to have a PI who is also a mentor. Are they invested in your success? Do they support you taking time off for career development? Are they open-minded to non-academic careers? A "no" to any of these questions is concerning.
Lastly, look out for the following Red flags. Any of these behaviors are serious and should not go ignored.
Does the perfect lab exist … hmmm …. perhaps not. Even if you are careful in choosing a lab, you may find yourself feeling unsure of your choice in the future. Start building a support system around you now. If a PI puts you in a difficult position, you'll be happy to have a supportive thesis committee and empathetic mentors outside of your lab to advocate for you.
Good luck this year! And as an academic, remember to stay positive and be kind.
Have you observed bright colored lights when rubbing your eyes? Have you seen transparent stringy particles floating midair when looking at the sky? Have you wondered if they are actually there? Or, are your eyes are fooling you? The answer is no; they aren’t there, but — your eyes aren’t fooling you either. These visual effects are called entoptic phenomena, derived from Greek, ento (within), and optic (eye). Therefore, entoptic means occurring within or inside one’s eye.
The renowned German scientist Hermann von Helmholtz once said, “under suitable light conditions light falling on the eye may render visible certain objects within the eye itself. These perceptions are called entoptical.” Interestingly, this phenomenon is purely subjective. They cannot be observed by an eye doctor using an instrument and cannot be photographed. Sometimes the phenomenon can be used to monitor eye diseases, but most occurrences are unconcerning. In this post, we discuss three commonly observed phenomena and how to differentiate these occurrences from the abnormal ones.
Rub your eyes by applying mild pressure using your index finger while keeping them closed. Do you see stars or circular shaped patterns moving opposite the direction of the pressure surrounded by bright multicolored lights? These patterns are called pressure phosphenes. We encounter them when rubbing our eyes upon waking up.
The word phosphene is derived from two Greek words; phos (light) and phainein (to show). This is the only phenomenon that occurs in the absence of light entering our eyes. We usually see things because light reflected off of surfaces enter our retinas, the backscreen in our eyes, and stimulate retinal ganglion cells that carry information to our brain to process what we see. So, how do we see light when there is no light entering our eye? Vision science researchers believe the mechanical stimulation caused by applying pressure on our eyes stimulates those same retinal ganglion cells. The cells think they perceive light, and we see several multicolored lights and shapes.
While seeing pressure phosphenes is normal, they should not be confused with flashes of light or aura seen in certain types of migraines and other conditions such as a posterior vitreous detachment or retinal detachment, where certain layers of deeper retina are peeling away. Phosphenes or star-shaped patterns can also be seen after a hard sneeze, a deep cough, a blow to the head, or low blood pressure as there might be mechanical or metabolic (low glucose or oxygen) stimulation of the visual nerve cells. These can also be perceived by meditators and by those who ingest psychedelic drugs.
Blue sheer phenomenon
Have you noticed a small number of circular or squiggly transparent shapes when gazing at the blue sky or on a uniformly bright background like a computer screen or a mobile phone? What do you think caused you to see them? Blue light from the sky enters our eyes and is blocked by red blood cells as they absorb all colored lights and allow only red light to pass. However, since white blood cells are transparent, they allow blue light to pass through them. This light further excites the retinal cells. So, the small transparent shapes we see are actually our white blood cells moving along the thin retinal blood vessels. As red blood cells are not transparent, we sometimes see dark patterns floating next to the transparent shape when observed carefully against a uniformly bright pattern.
Blue field or Sheerer phenomenon is observed only during daylight with open eyes and does not impair vision. However, this should not be confused with visual snow, where small white, black, or multicolored spots are seen in a television static fashion across the entire visual area for long periods. Visual snow usually presents with migraines, can impair vision, and is perceivable even when dark. While the exact cause is unknown, it is believed that visual snow is caused by excessive excitation of neurons, the nerve cells, in our brain and requires immediate medical treatment.
Floaters are tiny worm-shaped or transparent blobs that appear when you gaze at the sky or a uniformly bright background. Our eyes are made up of a transparent jelly-like component called vitreous humor that helps maintain the eye's shape and structure and helps keep the retina layers intact. With age, the vitreous humor gradually starts losing its transparency and viscosity. Due to this, the cells, proteins, and other components in the vitreous start forming clumps. When light passes through them, they cast tiny shadows on our retinas, called floaters. Seeing floaters in small numbers is normal, but it is alarming when you see large numbers of them constantly with a sudden onset. They could be due to a tear, detachment, or hemorrhaging of our retina or the posterior detachment of vitreous humor and require immediate medical treatment. Floaters should not be confused with blue field or Sheerer phenomenon as they are slightly longer in size and drift away with our eyes' rapid movements.
Entoptic phenomenon reminds us that what we see depends on the image created by our eye's physiology, i.e. the shape and structure of the eye and what we perceive in our environment. Hence, this should not be confused with optical illusions, which are purely caused by visual structures and are perceived differently from reality. So, next time you see some of these shapes floating, don't rush to rinse your eyes. Enjoy your observation with this new understanding.
The novel coronavirus, SARS-CoV-2, is the virus that causes COVID-19, a disease that has upended the entire world. Scientists have been working tirelessly to develop a COVID-19 vaccine. To control infection and also prevent further spread, entire nations are invested in the development of a safe, effective, and viable vaccine.
The timeline of the pandemic has been rapid, but so, too, has been the race to an effective and safe vaccine. Nidhi Parekh of The Shared Microscope and Sheeva Azma of Fancy Comma, LLC have summarized the key takeaways you need to know to understand the COVID-19 vaccine race. Read on to better understand the journey to a COVID-19 vaccine and the top contenders in this important endeavor.
When might a COVID-19 vaccine be available?
Things are heating up in the vaccine race. Several vaccines are in the clinical trials process, and many have reached Phase 3, the last stage before FDA approval. In late July, biotech company Moderna became the first to begin Phase 3 trials in the United States as a part of Operation Warp Speed, the US government’s effort to speed up the research and development process for a COVID-19 vaccine. Worldwide, Phase 3 trials were already underway when Moderna began Phase 3 trials in the US -- the Oxford/AstraZeneca vaccine has been in Phase 3 trials since early July in countries like Brazil and South Africa.
Top US White House science advisor, Anthony Fauci has predicted that a COVID-19 vaccine will be commercially available by early 2021. However, the US Food and Drug Administration (FDA) has the power to grant Emergency Use Authorization (EUA) status to vaccines well before then, if they are deemed safe and effective (to be used in high-risk populations, for example).
A variety of technologies and innovative approaches are being used in the race against the novel coronavirus pandemic. Because the entire world will need to obtain this vaccine, it is likely that many of these candidates will obtain approval in order to be quickly manufactured and distributed. In this post, we'll briefly discuss the vaccines from Moderna, Oxford/AstraZeneca, Sinovac, and Novavax.
Defining Viruses and Vaccines
Generally speaking, viruses cannot survive outside of a host. In the case of the SARS-CoV-2 virus that causes COVID-19, the virus uses humans as a host. Because COVID-19 is very infectious and spreads via respiratory droplets — such as by talking to someone without wearing a mask — the novel coronavirus was able to spread and proliferate worldwide.
When a virus infects a cell of the host, it is able to take over and use the resources of the host to replicate. After replication, the virus takes over the host cell to assemble new viral particles and infect more host cells.
Vaccines help stop the spread of viruses by helping humans develop immunity to them. Vaccines are used to introduce vital information about pathogens like bacteria and viruses to the body, in order to train the immune system to prevent future infection.
SARS-CoV-2 Spike Proteins are an Attractive Target for COVID-19 Vaccines
SARS-CoV-2 causes infection in people via spike proteins found on its surface. The infection that the virus causes is called COVID-19. The virus’s spike proteins help the virus interact with cells in our lungs (as well as other organs and even, perhaps, the lining of our blood vessels), to eventually enter and infect these cells. Once the SARS-CoV-2 virus is in our cells, thanks to the spike proteins, the virus can rapidly multiply and cause COVID-19 infection. Since spike proteins are vital to causing COVID-19 infection, the majority of vaccines in development are aimed at the spike proteins as a way to prevent a COVID-19 infection.
Three out of four of the top COVID-19 vaccine contenders (Moderna, Oxford, and Novavax) target the novel coronavirus's spike proteins, whereas a vaccine in development by Beijing-based biotech company, Sinovac focuses on culturing the virus in bulk and then “killing” or inactivating it with the use of heat or chemicals. These vaccines will all be further discussed in this article.
There are even more vaccines under development: you can check out the New York Times’ vaccine tracker for the latest COVID-19 news and updates. Below, we discuss four of the main contenders for a COVID-19 vaccine.
Moderna mRNA-1273: A Nucleic Acid Vaccine
Moderna Therapeutics is a biotech company based just steps away from Sheeva’s alma mater, MIT, in Cambridge, MA (USA). Moderna’s vaccine is based on molecular “messages” called messenger RiboNucleic Acid or mRNA. This messaging system is commonly used by the body to produce all the proteins necessary for survival.
The mRNA vaccine in development by Moderna contains instructions needed for our body to produce the SARS-CoV-2 spike proteins. When naturally infected at a later date, our body will have the tools necessary to scavenger-hunt the SARS-CoV-2 spike proteins as “foreign” entities and eliminate them. In other words, the vaccine will help our bodies develop immunity against the spike proteins.
The Moderna mRNA-1273 vaccine is currently in Phase 3 trials in the United States. To learn more about the vaccine, please check out this article.
Oxford/AstraZeneca ChAdOx1-nCov19 (AZD1222): A Viral Vector Vaccine
Oxford University in the UK has teamed up with AstraZeneca (also with corporate headquarters in the UK) to create a novel vaccine that is currently in Phase 3 clinical trials globally. Like the Moderna vaccine, the vaccine being developed by Oxford University, too, exploits the SARS-CoV-2 spike protein. This vaccine uses a non-replicating simian adenovirus as a vector - this means that the vaccine uses a replication-defective adenovirus (a type of virus) which causes cold-like symptoms in chimpanzees. The genetic material from this adenovirus is removed and replaced by the information to make only the SARS-CoV-2 spike protein.
Like before, the vaccine introduces vital information of the SARS-CoV-2 spike protein to our bodies, which helps flag the virus as “foreign” when naturally infected by it at a later date. Using the vaccine, our body has learned the viruses “top moves” and has the ability to cancel these. This allows the body to prevent future infection by the SARS-CoV-2 virus.
Oxford/AstraZeneca have received approval to complete phase 3 trials in Brazil and South Africa. We hope to receive the results of these trials by Fall 2020.
We have previously written about how the Oxford/AstraZeneca vaccine works in more detail, as well as what it's like to participate in the Oxford vaccine clinical trials over at our blog.
Novavax’s NVX-CoV2373: A Protein Subunit Vaccine
Novavax is a biopharma company based in Germantown, Maryland (USA), not too far from Washington, D.C. The vaccine in development by Novavax, called the NVX-CoV2373, is a protein subunit type vaccine. This means that the active ingredient of the vaccine is a protein. More specifically, the protein of interest is the SARS-CoV-2 spike protein. The spike proteins used in the Novavax vaccine are grown in the laboratory, and then harvested. The spike proteins are then purified to filter out any unnecessary molecules, and used in a vaccine.
Again, the spike protein will be identified by our bodies as “foreign,” and then an attack will be planned against these proteins, to then ensure safety from any future infections. Novavax has received $1.6 billion in funding from Operation Warp Speed. They have since seen their stock prices rocket from $5 to $130 dollars, making it an attractive target for investors.
The vaccine in development by Novavax is currently in simultaneous Phase I/II clinical trials in South Africa. Learn more about Novavax and how it works here.
CoronaVac: An Inactivated Virus Vaccine
The CoronaVac vaccine is being developed by Chinese biopharma company Sinovac. CoronaVac contains an inactivated version of SARS-CoV-2. As a vaccine of the inactivated type, this vaccine relies on a tried-and-true method of vaccine development. The COVID-19 vaccine is made from harvesting whole SARS-CoV-2 viruses and then chemically inactivating (killing) them.
The CoronaVac vaccine has received approval to conduct phase 3 trials in Brazil, the results of which are currently awaited. Learn more about CoronaVac here.
In the COVID-19 Pandemic, Knowledge is Power
Knowledge is power! This stands 100% true amid a pandemic. Knowledge about the COVID-19 vaccines will help combat misinformation and eradicate dangerous ignorance. While many may be fearful of the new vaccines, building understanding can help reduce fear and anxiety, which are driving anti-vax sentiment that threatens to derail all of humanity’s great efforts to overcome the pandemic and many other preventable life-threatening diseases.
You can learn more about the science of COVID-19 vaccines, and more about the ongoing COVID-19 vaccine trials in general, at the Fancy Comma website.
Bolded Science supports a healthy work life balance and self-care of scientists everywhere — that includes myself! It's summertime in Connecticut and after months of publishing weekly posts, I am taking a well deserved break. Bolded Science will be returning in September for more posts by members of the scientific community!
Are you looking to add more writing samples to your sci-comm portfolio? Do you have a science-related cause you'd like to advocate for? Are you conducting super interesting research that you are just dying to tell everyone about? Pitch a blog post to Bolded Science: TheBoldedScientist@gmail.com. It's simple, send an email introducing yourself and 1-2 sentences explaining what you'd like to write about. Then, we will pick a publish date. Once you are approved, write your post and email it to me 2 weeks before your publish date.
Questions? Please see the FAQ page: https://www.boldedscience.com/faq.html . Question not there? Please send an email and I'd be happy to help.
Thank you to all readers and writers of Bolded Science. This collaborative blog is made possible by our curious, knowledgeable, and passionate community of scientists. In less than one year, Bolded Science has grown to have > 2,000 twitter followers, thousands of post reads, and over fifteen writers. I look forward to working with more of you this fall!
Accepting blog posts for the following publication dates:
All Thursdays in October
Kerry Silva McPherson
Creator and Editor of Bolded Science
PS: Please be patient with email replies, I'll be only checking my inbox a couple of days in the week.
An email buzzed my phone: Volunteer Meeting at 4 pm. I smiled. It was that time of the year again. The silent maze of aisles wrapping our labs will come alive with bustling curiosity, eyes glazed in awe of the grandness of all the shiny things around, heads and hearts absorbing everything the ears get to hear. "Soon," I said to myself. "Hey, Google, set a reminder to go to the auditorium at 3:50 pm". I smiled throughout the entire day. Memories. Ideas. More memories.
Planning and Creating
Just a few months into my PhD program, I was introduced to Open Day - a day when a research institute, university, or any place usually beyond the access of the general public throws its doors open for engagement. One of our faculty members organizes our Open Day each year with fresh PhD students at the helm. 2015 was our turn. She briefed us about the various workshops, exhibits, tours, and activities that are undertaken this day and how it is done. Participation was voluntary. Yet many among us jumped in.
Preparations began days before the actual event. Responsibilities were effectively delegated. Creativity was on full throttle. Volunteers designed attractive posters and handled emails and social accounts, spreading color far and wide. People who would manage coordination on the floor created detailed route maps for the shepherds, allocated time slots for each activity, and checked-in on others' progress. The many volunteers who would run the show were busy building exhibits and models, gathering material for workshops. The zeal that steeped the usual academic air became more palpable as the event drew closer for volunteers and non-volunteers alike.
Even though the general public is welcome, open days are primarily attended by school students, escorted by their schoolteachers in groups of 20-40. They are split into groups, each group assigned to a shepherd volunteer to take them on an intellectual joyride. Footfall came by the hundreds and filled the entire institute. If one were just to walk around, the variety would amuse them.
Visitors can ask many questions, and observe science they may have never seen previously. Volunteers explain how machines work. There is a stall where participants can take home their own DNA as a souvenir. And visitors can view a model demonstrating how neurons send messages or an exhibition of how movement of objects can be triggered by light. Open Day is like a huge science fair with a mix of kids and adults. Younger participants' playful curiosity is contagious.
That year, a few other batch mates and I aimed to carry forward a popular workshop from last year – Tod-Phod-Jod (Break-Burst-Join!), an activity that familiarizes kids with computer parts. A bunch of bioinformatician fellows handed out non-functional laptops and peripherals like a mouse (generously donated by colleagues and staff) to disassemble and reassemble, getting to know the various parts as they went along. We inherited some leftover machines from 2014, but they wouldn't suffice for hundreds of children. Our calls for more defunct machines met no end. We had to improvise. But none of us were bioinformaticians. Any idea we came up with did not connect well with the previous theme.
With time slipping out of our hands, we thought it better to 'break' the mold. Learning a few science tricks off the internet, a range of demonstrations were planned. We were given 45 minutes to conduct the workshop per group. Our sole purpose was to engross the attendees and generate sustained interest in all-things-science. We wanted them to exit the workshop wonderstruck. Twenty minutes of disassembly & demonstration of a gadget. Fifteen minutes of tricks based in viscosity, energy transformation, and fluid dynamics. Ten minutes of Q&A. And lastly, a 4-minute video on sixth sense technology. That ought to do it. "Each stall will see a minimum of three to four hundred students," the faculty's words rang in my ears. Would we be able to deliver? Anticipating a full house, we entered that dawn with our fingers crossed.
Early on the event day, we spent time debating whether the children should be allowed to disassemble the gadgets at first. Most of us gave in to the conviction of the teammate in charge of the demonstration. Wary if we would manage to reassemble the laptops before other groups entered, we ruled in favor. The first two rounds went as planned. But the crowd swelled soon after early-bird hours, and there was no buffer time to reassemble the components back into a computer. Before we knew it, we were catering to two groups at once! Anyone would have expected the demo to derail. Eventually, each team member got busy playing their part. Were we losing it as a team? Was the workshop going to be a mess of disjointed tasks?
Adrenaline. Rushing through. All senses on high alert. I noticed the computer guy had changed his narrative. Now, he was just showing the parts to the students and where they fit in the computer and what they did, asking them to guess what the piece was! The kids scrambled to answer first. "Me! Me!" each shouted. And it continued. Once through, he asked them to guess the next section of the workshop, keeping them intrigued.
Science or Magic?
One after the other, they watched the tricks. Some gasped in amazement, some exclaimed. No one was uninterested. We would ask them, "How do you think this is happening?" and skim their guesses for accuracy. As if by a divine intervention, just once, my teammate doing the trick responded, "No, all your guesses are wrong. I am doing magic!". That left the students dumbfounded for a moment. I intervened with "Magic is nothing. There must be a reason! There's science behind everything", coaxing them to examine the setup of the trick. Within moments, some students came up with the answers:
"This water is hot, and the other is cold!"
"What's this liquid? It's not water. It's very sticky."
Temperature affects density. Sugar increases viscosity. Round after round, each group of students called out the magic hoax. Our magic was done. The video on sixth sense technology showed them how science could, in its own time, make 'things of fiction' real. All the students promised to go back and explore more of science in everyday life
Having catered to at least 12-15 such rounds in that one day, interacting with 300 students, we were exhausted and bedazzled. We made it - Tod-Phod-Jod was a popular workshop in later years, too.
Since that first experience, I participated every year. Open day became my sole doorway to the public domain where I can bust myths, ignite curiosity, and educate others about the ways of science and research in a direct and engaging manner.
Science, a way of life.
It was that time of the year again. 2019.
"Which scientist do you want to name your group after?" she asked me.
"Rosalind Franklin," I answered.
I'll tell them the story of Rosalind Franklin, give them a taste of 1950s Europe, and then stress the role of evidence in the quest for truth. By sharing true stories, I'll convince them to look for proof. Always. In everything. Science is, after all, a way of life. And I'll tell that to anyone and everyone I can — a few, or many, at a time.
In public arguments about controversial topics, one often hears the somewhat pugnaciously offered challenge: "Do you have a reference for that?" Meaning: Do you have a peer-reviewed confirmation of what you are saying, published in a reputable scientific journal? Providing such a confirmation usually lowers the temperature of the discussion somewhat.
Now, factual statements should certainly be backed by convincing factual evidence – that is the whole point of the empirical scientific approach. But apart from ignoring the difficulty that factual evidence means something rather different in, say, particle physics than in psychology, simplistic efforts to "have science on one's side" degrade science in the public eye to a caricature of itself, a stodgy guardian of indisputable facts, a records clerk. It is worth reminding ourselves that science is no such thing.
Far from being a boring fact-monger, scientific inquiry owes a profound debt to imagination. After all, the very idea of investigation is an exercise in speculative thinking, since someone must first wonder what is there to see in the depths of the sky before a telescope is actually trained at the stars. And beyond that indispensable moment of "What if?" which goes before any investigation, significant and far-reaching discoveries have often been a result of thinking in an adventurous direction. Let me recall a few from the history of my favorite science, physics.
In the face of the failure of all known physics to account for the radiation spectrum of a glowing furnace (the proverbial "black body"), Max Planck made the seemingly wild conjecture that perhaps the radiated energy comes in discrete packets, quanta. Planck had no "reference" for that, and nothing in the observed radiation spectrum cried out for that particular conjecture. But when he applied it, it described the spectrum perfectly, and of course, Planck's conjecture went on to be the central insight of all of quantum mechanics.
Similarly, Albert Einstein grappled with the thorny problem of reconciling the venerable discipline of Newtonian mechanics with the younger but very convincing theory of the electromagnetic field. These two theories differ in their mathematical structure and physical implications, and they could not both be correct. Einstein is said to have contemplated at length what it would be like to ride on a beam of light (an electromagnetic wave), as one would ride in a plane or a spaceship. To make the story short, it turns out that we, being massive objects, could never attain that speed. Moreover, on the beam of light there are no distances in time: to the light everything happens at once. The intuitive and well-established mechanics of Newton proved to be unsuitable close to light speed, and Einstein's improved description of the world is now known as special relativity.
Another notable contemplation of Einstein's was, "Why do things have only one mass?" The mass of an object manifests itself in two ways: as inertia in free motion, and as weight, the gravitational attraction. On the face of it, these two phenomena have little in common, yet the forces, accelerations etc. all speak of one and the same mass. Why should that be? Why are things that weigh heavy on the scale also sluggish to speed up? This counter-intuitive question led to the insight that gravitational pull is "free motion" in the space that is itself bent by gravity, the core insight of general relativity.
(Many introductions to the theories of relativity have been written; one of the more approachable and lucid ones can be found in this charming book.)
Vortices in thin air
There is, however, a difficulty with brilliant imagination: it does not in itself mean that you are right. In the waning days of pre-modern physics, the prevalent opinion held that the light, the electromagnetic wave, propagates by means of an invisible, tenuous, frictionless, non-viscous fluid called luminiferous aether. Every other kind of wave was known to need some material stuff to propagate through, so the aether hypothesis was a plausible but not very insightful reasoning by analogy – with one possible exception.
Vortices in an ideal fluid are eternal, and their lines of swirl cannot be broken. A "smoke ring" in aether remains a ring forever; a knotted vortex loop can never be untied, and so on. Physicist William Thomson (Lord Kelvin) hypothesized that there might exist primordial vortices in the all-pervading sea of aether: there would be various types of them, differing in their properties according to the topology of the knots they formed, eternal and immutable. They would be the atoms of matter.
In reality, ever more extravagant properties had to be attributed to the luminiferous aether in order to explain how it could carry the electromagnetic wave, and the aether finally evaporated in the historic Michelson-Morley experiment. Thomson's hypothesis of atomic vortices evaporated with it, and in any case, the actual atom turned out to be something quite different from a knotted vortex. All the same, one cannot but admire certain daring cleverness of this idea, bringing together the subtleties of fluid mechanics and topology in an attempt to account for something seemingly unrelated: the existence and varied properties of atoms. It would have been remarkable had it turned out to be true.
Of course, the correct theory of the atom, the quantum mechanics, more than compensates for this "loss" with its own remarkable subtlety. But we can hear the echoes of the vortex theory in the speculative ideas of our own time: such as the string theory, which posits that the ultimate building blocks of the universe are not dot-like but line-like; or the idea of the space-time as a "quantum foam" teeming with the fluctuations of the quantum uncertainty principle. These are attempts to stretch our current understanding of physics beyond what we can observe at present, in order to explain things we still don't understand, chiefly how gravity and quantum mechanics fit together. Only future experiments will decide whether these conjectures describe something real, or are they merely clever flights of fancy, like Thomson's vortices.
Imagination in a straitjacket
This brings us to a remark by the physicist Richard Feynman, who once gave a memorably succinct description of the scientific process: he called it "imagination in a straitjacket." What Feynman meant is that, as scientists, we accept that all insights, however flighty or clever, must eventually be subjected to the straitjacket of the experiment, of empirical verification, for that is the great strength of science.
But on the other hand, we also know that imagination withers in a straitjacket: overly constrained insight loses courage and gradually gives way to low-risk squabbles over evidentiary minutiae. In contrast, it is the inevitable fate of any far-reaching understanding that it skates on thin ice of evidence, because the methods of observation have yet to catch up with it; the right straitjacket has yet to be devised. As another historical example, irrefutable evidence of evolution was not available to Charles Darwin in his lifetime, nor was molecular genetics, nor computational modeling of evolutionary processes; still, his elegant insight into the dynamics of living things has withstood the test of time.
So perhaps we should refine Feynman's dictum. The jacket is beneficial and necessary because it protects empirical truth from error, deliberate falsehoods and outright quackery. Moreover, when experiments that would answer crucial questions are beyond practical reach – when an adequate jacket cannot be devised, as is currently the case in much of the fundamental physics – extravagant speculative theories begin to proliferate freely, as they once did in the days of the luminiferous aether.
But the very accumulation of knowledge inexorably tightens the straitjacket: as a scientific field matures, progress becomes constrained by what is known, and runs the risk of becoming risk-averse and timid. In this light, we should uphold the importance of imagination and creativity, and defend their legitimate place in the ongoing dance of conjecture and verification that is the scientific enterprise. Not every age is conducive to mind's grand adventure, and not every daring idea is true. But should we all be content merely to safely reference each other's impeccable results? Without answering the seductive call of the unknown and the adventurous, where would new knowledge come from?
Accessibility tends to be a major topic in regards to science communication (sci-comm). However, most of the time, people only refer to making the content accessible to the general public, neglecting to take into account those with disabilities. Considering the audience is essential, but your considerations need to extend beyond using plain language and no jargon. It's also necessary to commit to the idea that science should be accessed and understood by everyone. This is not a new issue; however, it has become more apparent due to the increase in sci-comm demand during the Covid-19 pandemic.
In this piece, I will go through the formats that are commonly used for sci-comm and highlight the most important accessibility points. I will also assess different social media platforms that can be used if applicable to the format. Hopefully, the information shared here can be incorporated into your own work to make your sci-comm accessible to all.
Videos are a popular method of virtual sci-comm as they make information more interactive. This may be obvious, but adding captions or closed captions to your videos and/or providing a text transcript is a great help to the hearing impaired and those with learning disabilities. What's the difference between closed captions and captions? Closed captions include subtitles and a description of anything you hear in the video. Captions refer just to the subtitles, which assume that the audience does not have hearing impairments.
A simple method to achieve this is to use YouTube, which automatically generates captioning of the video that you can edit to correct mistakes and add descriptions as needed. You can even add commonly used words (i.e.) chemicals, reactions, names, etc., to your channel settings to minimize errors. The video with captions can then be shared to other platforms.
Another video sharing platform, Vimeo, requires closed captions to be uploaded as a separate file (e.g.) SRT file, in the settings. Facebook and LinkedIn have similar formats to this.
There are also closed captions or caption apps like Caption This, InShot, and Clipomatic. However, the reviews of these apps are mixed, so do your own research. Another option is to add captions manually using online or downloadable media tools such as Subtitle-Horse or Camtasia Studio.
2. Live Streams
Live streams can be used across several different social media platforms, and similar to videos, they need closed captioning. If enabled, YouTube provides automatic captions for live streams. Again, if you add your commonly used words to the settings, then it can be reasonably accurate. Zoom has an option for someone to type subtitles as the conversation is happening, but can also facilitate a third-party caption service if the conversation will be too fast for someone to type.
Facebook Live can facilitate close captioning, but only with the use of a third-party caption service or an external automatic caption generator. Similarly, Twitter can also facilitate an outside automatic caption generator for live streaming.
While researching for this piece, I discovered that you can now live-stream from LinkedIn! However, there is no option to provide captions. Similarly, Instagram does not have any facility for live closed captioning.
3. Blogging and Presentations
Blogging via a website is another popular sci-comm method. The layout is essential here. It is recommended to avoid multiple columns on a webpage, as screen readers can get confused. Screen readers are an assistive technology for the visually impaired that converts content (text, alt text, transcriptions) into speech or braille. If you are using a blogging platform, it's important to use the 'Heading' options when formatting. Screen readers do not understand that people just make the font one size bigger or tab in once to mean a new section.
For the rest of this section, the points apply to presentations and blogging as the issues can be similar. Poor color contrast between backgrounds and text can be a huge problem. Be extremely cautious about using background images, especially busy photos. Using color contrast tools to assess your webpage can help you avoid this issue (e.g.) Webaim Contrast Checker, and ACART's Contrast checker. You can also create color palettes for general use on coolors.co.
Fonts are also a critical choice for accessibility. There is a font that has been designed for dyslexics called Open Dyslexic that you can download. Although research has found that there is no significant difference between this font and some Sans Serif fonts in terms of readability for dyslexics, so it's not essential. The Sans Serif fonts recommended are Comic Sans, Open Sans, Arial, Verdana, Tahoma, Century Gothic, and Calibri.
The British Dyslexia Association recommends font size 12-14 and 1.5 line spacing for optimum readability of websites. I have never seen an official guide for presentations, but my own rule of thumb is at least font size 20 and 1.5 line spacing.
Finally, if using images, graphics, graphs, or related, always provide a caption or description for them. It is also necessary to describe all visuals when giving a verbal presentation, something many people forget.
4. Graphics, Infographic, and Posters
Many people like to make their own graphics, posters, or infographics to get their message across; they are great but unfortunately are not very accessible. All graphics need to follow many of the same rules for webpages and presentations in regards to color contrast, fonts and spacing, and captions to maximize readability.
It was pointed out to me recently that screen readers cannot interact with infographics posted on social media or a webpage. This absolutely makes sense as they are graphics, but this is easily overlooked. Please always provide a detailed transcript of all information and graphics on an infographic to make them fully accessible.
5. Social Media Posts
Your content, itself, is now accessible, but what do you need to know about posting on social media in an accessible manner? What do you need to change to expand your reach and maximize your impact?
As I have already mentioned, it's essential to provide a description for any visual material. This can be done on Twitter and Facebook by clicking 'edit' on the uploaded image and filling in the 'alt text'. Facebook autogenerates descriptions if this is not filled in, but twitter does not. Instagram also autogenerates descriptions that you can edit by pressing 'Advanced Settings' before you post. However, autogenerated graphic descriptions are not recommended as they tend to be basic. It is also much easier to understand if you include the format the image is in (i.e.) [Gif], [Photo], [Graphic]. This is also relevant for links and hyperlinks. If you are using links, specify where they will lead (e.g.) [Website], [video], etc..
Finally, Hashtags – yes, hashtags. You need to capitalise the first letter of every word in a hashtag, or else a screen reader will read it out letter by letter. Imagine how annoying that can be! It's something straightforward that makes a big difference. Just post #ScienceForAll instead of #scienceforall.
In general, try to be considerate and include the general public with disabilities in your sci-comm. Also, this piece is not exhaustive, there are many other ways to make your sci-comm accessible. Accessibility should be built into the design, not an afterthought or a last-minute addition. You don’t have to be perfect from the get-go, you will improve with time. The most important thing is to try and take feedback.
After weeks of quarantine, universities are ramping up research, allowing scientists to continue their fieldwork and benchwork. For many of us, returning to the lab brings mixed feelings. Personally, I want to continue my research. But on the other hand, I haven’t missed the sensation of messing up an experiment or the agony of waiting for results.
Weeks of isolation have allowed me to think about what I want from my career. And many of my colleagues are pondering the same. As the scientists return to the bench this Summer and Fall, they are bringing a new attitude and perspective with them.
Flexibility in the workweek
The pandemic proved that when research is stalled, the world continues to spin. A truth that might seem obvious to an outsider, it was none-the-less a revelation to me. A setback in experimentation is common, an expectation more than an exception. But still, the slow creeping pace of science instills guilt in many graduate students and post-docs. To compensate for failed experiments and confusing results, we scramble to fit as much work into a week as possible, often working on weekends when we arbitrarily feel like we are falling behind. The long nights, weekend work, and obligation to hold a 9-5 schedule add up to a long workweek, which might, in fact, be less productive than we perceive.
Working more than 40 hours a week is correlated with poor performance and health issues. And although numerous companies have experimented with <40-hour workweeks and experienced beneficial results, many still believe the traditional workweek + overtime is the standard for a “hard worker.”
I regrettably have no studies to cite about the productivity of laboratory scientists vs. hours worked. But I do have less-substantiated anecdotal evidence. Since returning to the lab, I have not worked a 9-5. Instead, I let my experiments dictate when I come into the lab, and I set a reasonable expectation of the amount of reading and writing I should accomplish in the week. As a result, I take detailed notes in my lab notebook, I have time to address setbacks, and I have less failed experiments.
Prioritizing career development
Contrary to some academic’s beliefs, there is more to a CV than publications and conference presentations. To be a desirable candidate upon graduation or completion of your post-doc, one must pursue opportunities in your anticipated field actively. To the dismay of some of our PI’s expectations, that might take time away from our work responsibilities.
Although my experience may differ from many, I rocked at career development during the quarantine. I am playing towards my strengths and passions and am pursuing a career in either science writing or science policy. For both career paths, honing my writing skills is imperative. When working from home, it was easy to dedicate time to writing and editing. But continuing my writing ventures and returning to work will be a challenge.
Challenge accepted. Career development, whether it be learning to code, taking business classes, or teaching, is imperative to your education. Therefore, as a pre or post-doctoral trainee, continue to schedule in career development time to ensure you have a competitive resume when your training is complete. This may require you to jeopardize time at the bench, but as I mentioned in the previous section, time does not equate to productivity.
Mental health care
We all struggled with mental health in isolation. The uncertainty brought about anxiety, lack of socializing led to depression, and boredom cultivated alcohol abuse. Unfortunately, returning to work does not guarantee an instant bounce back for our mental health. As we return to the bench, we must safeguard our well-being.
Working a flex schedule and seeking quality over quantity, as mentioned above, is one avenue to nurturing our mental health. Additionally, working from home does not mean you cannot take time off this year. Quarantine was not a vacation. Spending time away from your home and work can help give you the energy and positive outlook you need to perform well in the laboratory.
Training as a scientist is certainly a journey. Choosing to fixate on the end-goal — the publication, the graduation, the defense — is a breeding ground for disappointment. Timelines in the laboratory are ambiguous and often out of our hands. This has only been exasperated by Covid-19. Your goals will likely not be met when you want them to, so it's important to shoot for results you have control over.
Focus on the small goals — learning a new technique, working on one chapter of your thesis, optimizing an experiment. Plan for the future, but don't live in it. Enjoy where you are now.
In this post, I’ve shared my perspective on how lockdown has changed my career mind-set. But I am aware that many other scientists’ experiences vary. The lockdown was welcomed by some, an opportunity to slow down and take a break from a sometimes-toxic workplace. Others resented being barred from the lab. In an earlier Bolded Science post, we learned how some scientists couldn’t bear being away from their treasured workplace and found creative ways to conduct science at home.
Scientists will have various feelings about research ramp-up as well. Some co-workers might need time to acclimate to a new routine; others are anxious to make up for the lost time. Be mindful of our differences. As we reopen, let’s practice thoughtfulness and kindness at work. When Covid-19’s prevalence lessens, the impact is here to stay.
*Names are altered for anonymity
As I entered the lab after lunch, Geeta,* a master's dissertation trainee, was being scolded by her mentor, Rakesh*, for not reading up when he told her to. Her ears had turned red, tears brimming her eyes. She left almost immediately as more people poured in. Although an average student, Geeta is sincere but rather meek. Her neglecting to read felt strange to me. Plus, Rakesh is known for his impatience and temper. Some nudging revealed that Geeta had read but couldn’t explain it to Rakesh. So he started shouting. And then she went blank.
Where I study, such scenes are common during the spring session with new doctoral aspirants and master's dissertation trainees abound. Fresh students grapple with the unstructured, scattered learning methods of real-life research and existing PhD scholars largely distance themselves from the role of a trainer/mentor. There is no formal “train-the-trainer” coaching, hardly even an informal discussion. There aren’t any “orientation sessions” to ease the newbies into the esoteric environment. Such unpreparedness leads trainees to doubt their capabilities and junior mentors to be clueless about what “picks up” their mentees. It sounds like a perfect recipe for disaster.
But we do not witness many disasters around us. Thanks to the autopilot. The emotion of autopilot has one aim - defense; to preserve our sense of self. This psychological tool called the “fight or flight response” derives from our primal instinct of surviving physical danger. It fulfills its goal very well but as a side-effect, it perpetuates an undercurrent of nervous energy that scans our environment for threatening events. In Geeta and Rakesh’s scenario, Geeta’s psyche will try to ‘flee’ such interactions through avoidance. If the same pattern reoccurs, her psyche will come up with ways to never interact with Rakesh. In case the interaction is necessary, her fears will play out in other ways. There’s very little chance that she’d actually learn anything in this process.
Being prepped up at all times to respond to a perceived threat can be draining and in the long run, it is counter-productive to stay on autopilot. There are two ways to break this stalemate - either Geeta has to ‘suck it up’ and deliver or Rakesh has to modify his training approach. Neither of them can be done while they’re both on autopilot. Here, we find ourselves staring at a problem - and it is not the autopilot. It is, in fact, a built-in response to the underlying problem(s).
Do all problems really have a solution like novelist, Alice Hoffman, says? The philosopher, John Dewey, said a problem well put is half solved. So let's begin there - defining the problem. We’ll have to take a couple of steps back to get to this one. Walk with me.
Flashback: College days are memorable for most of us. We’re young and everything seems possible. New friendships blossom, career opportunities abound. Academically, all we need to do is score reasonably well on tests. The syllabus is well-defined, lectures and classes help you learn. Umpteen sources are at your service. Sports and extracurricular activities take our minds away from academic demands from time to time, giving us breathing space. By design, we get much needed breaks. Students may sustain despite slacking on studies once in a while. In short, we are carefree for the most part.
Flash-forward: A research laboratory. In many ways, here, you are your own boss. You are solely responsible. This environment is a deep contrast to all previous educational settings. As opposed to timetables and syllabus, you will have a research aim and more or less nothing else. Not only do you have to create your own checklists (in a gently guided way, if you are lucky), you have to find ways to effectively complete them. That takes a serious amount of time devoted to self-learning. The linear ‘read-rote-repeat’ model fails miserably in this arena. If you have conceptual understanding in place of rote learning, you are fortunate. Still, you would need to cope with the lack of structure in your reading resource here. After all, to get good at pulling out useful research articles AND read them critically is an art. The motive is to read, understand, infer and then apply your understanding towards the project. Now this is a cyclic process, instead of the linear one you’re used to. Over that, seldom are there any check-ins as you follow this multistep process.
Application of knowledge boils down to experimentation - the technical part of research. Getting hands-on handling instruments, reagents, living material, etc for the first time means fertile ground for mistakes! There will be times when there’s no one around you to advise how to fix it, or tell whether it is even fixable (Your soul will be grateful for Google that day). Learning from failure and moving on like it was never a thing is the number one survival skill you’ll have to develop.
Copious amounts of literature might remain pending on your checklist as you set up that next experiment (or another trial at a failed one). You might have to execute a procedure when you aren’t completely sure of it. All the while, the clock is ticking. Unless you were always inherently great at it, time management becomes an overwhelming task. Time will be your most precious commodity because it feels as if it has shrunk.
Whether you are a fresh new researcher or mentor, taking a few steps towards each other will take us a long way. It’s never too late to make academia a better place. Shall we?
You order take-out at your favorite restaurant over the phone. You then drive to this restaurant, park your car, go inside and get your food. But haven't you wished that all restaurants had the option of a drive-through window? You save time, and it is indeed way more efficient.
Similarly, tiny cells in our body have their own version of drive-through windows, specialized structures known as 'porosomes.' However, unlike restaurants, every cell has several porosomes embedded on their outer covering, the cell membrane. The porosomes are tiny and cup-shaped, in the size range of nanometers, you could fit at least a 1000 porosomes on the tip of a single hair strand! The word 'porosome' literally translates to pore-forming bodies. They open and close, aiding in proficient cell secretion, just like a restaurant drive-through!
Wait…but what is secretion?...
To understand secretion, we need to know what cells are, and for that, we need to understand how animals are organized! Throwback to our school days, we learned that animals are made up of organs like the heart, brain, lungs, and many others. Each organ is made of tissues, and every tissue is built out of cells, so technically speaking, cells are the basic unit of life. Cells need to communicate with each other and their surroundings to keep an animal functional. They do so by releasing chemical messengers into their surroundings, and this process is known as 'secretion.'
Secretion is a universal phenomenon; almost all cells secrete at a basal level. But certain types of cells are specialized for secretion. These cells are critical for simple life processes such as thinking, digestion, building muscles, and energy production. Porosomes are thus present on cells that undergo secretion as their primary function. Furthermore, defective secretion by cells can lead to diseases; for example, Diabetes may be caused when β- cells of the pancreas fail to secrete the hormone, insulin.
So, how do porosomes know that a cell wants to secrete?
An extremely complex process turns on a switch within cells that causes them to secrete. Once the switch is on, it sets the 'secretory granules' in motion.Secretory granules are spherical bags within cells that carry chemical messengers such as insulin. During secretion, the secretory granules travel from the center of the cell towards the cell membrane, on which the porosomes are located.
The base of porosomes has a dedicated machinery that anchors secretory granules until they have released their contents. Once a granule latches on to a porosome, the porosome opens up, facilitating the release of chemical messengers. The porosomes, therefore, establish a connection between the granules and the cell exterior, similar to a drive-through window.
Cool! What else do we know about these porosomes?
Porosomes were discovered pretty recently in the early 1990s, and there is an interesting story to their discovery. Conventionally, it was believed that granules fuse to the cell membrane during secretion. But this couldn't explain some crucial observations made by scientists. Firstly, high-resolution microscopic images of cells after secretion show that granules still have chemical messengers left inside them. Secondly, imagine, if all the secretory granules fuse with the cell membrane, then cell size and volume must increase, which wasn't witnessed. Lastly and importantly, the secretory granules are very similar to soap bubbles. They are spherical, have a high surface tension, and pop as soon as they come in contact with a surface. Therefore, granules may find it difficult to merge with the cell membrane without exploding. So, a porosome structure was suggested and later discovered that prevents granule collapse.
Neurons of the brain, cells of lungs, and β- cells of the pancreas are all equipped with porosomes for secretion. Although similarly shaped, every cell type has porosomes that are distinct in size, make, and design. For instance, porosomes from brain cells may be unable to secrete insulin.
Recently, porosomes were fished out from β-cells of mouse pancreas and inserted into living cells of the same type. The newly engineered β- cells had extra sets of porosomes embedded on their cell membranes. These cells were able to release more insulin than usual. Although further research is required, this could be a potential therapy for mitigating, not just Diabetes but many other secretory diseases.
Another secretory disease is cystic fibrosis (CF), which occurs when lung cells have faulty fluid secretion due to the sub-optimal function of the CFTR protein. Interestingly, when separated from lung cells, CFTR was found attached to the porosome suggesting that reconstitution could be a potential treatment for CF patients too.
Porosomes, although tiny, have made a mighty shift in the way we now comprehend cell secretion.